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Published on: May 7, 2010
Inconsistencies between human genetic cytolocations and those derived using genomic sequence
A J Cuticchia1, R D Kulkarni, W E Parris
1Research Triangle Institute, Research Triangle Park, NC 27709, USA. ajc@rti.org
Cytogenetic and Genome Research
|November 9, 2005
Summary
The human genome sequence enables gene mapping but creates discrepancies between genetic references and computational locations. 18% of gene records show differing cytogenetic band locations, impacting biological database utility.
Area of Science:
- Genomics
- Bioinformatics
- Human Genetics
Background:
- The publication of the human genome sequence allows for gene identification via genomic positioning.
- This has led to a divergence between traditional genetic references and computationally derived gene locations.
- Discrepancies exist in the cytogenetic band assignments for human genes.
Purpose of the Study:
- To quantify the extent of discrepancies between published cytolocations and computationally derived genomic locations for human genes.
- To assess the impact of these data inconsistencies on the usability of integrated biological databases.
Main Methods:
- Comparison of gene records from Mendelian Inheritance in Man (MIM) and Ensembl.
- Analysis focused on records sharing HUGO gene symbols.
- Identification of differences in cytogenetic band locations between the two datasets.
Main Results:
- A total of 6,830 gene records with shared HUGO gene symbols were analyzed.
- 18% of these records exhibited a discrepancy of at least one cytogenetic band.
- This highlights a significant level of discordance between genetic and genomic data sources.
Conclusions:
- The frequency of discrepancies between cytogenetic and genomic gene locations is substantial.
- These inconsistencies pose a significant challenge to the utility and integration of biological databases.
- Standardization efforts are needed to reconcile differing gene location data.
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